Variant report

Variant	rs2279473
Chromosome Location	chr5:92932305-92932306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:92931819..92934085-chr5:92938375..92940060,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR2F1-5	chr5:92932191-92933236	l_2975_chr5:92932190-92934697_testes

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10036024	0.82[MEX][hapmap]
rs10038831	0.86[JPT][hapmap]
rs10041792	0.86[JPT][hapmap]
rs1004941	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs10050364	0.84[JPT][hapmap]
rs10051878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10060331	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs10067541	0.86[JPT][hapmap]
rs10071040	0.86[JPT][hapmap]
rs1038686	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs1046217	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10476520	0.86[JPT][hapmap]
rs10514376	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs11959119	0.91[EUR][1000 genomes]
rs12186735	0.86[ASN][1000 genomes]
rs12186878	0.86[CEU][hapmap]
rs12187239	0.93[ASN][1000 genomes]
rs12188716	0.86[ASN][1000 genomes]
rs12188905	0.93[ASN][1000 genomes]
rs13154650	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs13161885	0.86[JPT][hapmap]
rs17082127	0.86[ASN][1000 genomes]
rs17082129	0.86[ASN][1000 genomes]
rs17083181	0.86[ASN][1000 genomes]
rs17083191	0.93[ASN][1000 genomes]
rs17083194	0.93[ASN][1000 genomes]
rs17083198	0.93[ASN][1000 genomes]
rs17083200	0.93[ASN][1000 genomes]
rs17083213	0.93[ASN][1000 genomes]
rs17083228	0.93[ASN][1000 genomes]
rs17083278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs17083297	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17312456	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17370695	0.86[ASN][1000 genomes]
rs17372615	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17372649	0.86[JPT][hapmap]
rs1824153	0.86[ASN][1000 genomes]
rs1844343	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2083227	0.86[ASN][1000 genomes]
rs3776601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57690257	0.86[ASN][1000 genomes]
rs57924239	0.86[AMR][1000 genomes]
rs58143801	0.80[ASN][1000 genomes]
rs58237393	0.80[ASN][1000 genomes]
rs58919600	0.81[AMR][1000 genomes]
rs59360932	0.93[ASN][1000 genomes]
rs61324921	0.86[ASN][1000 genomes]
rs61352323	0.93[ASN][1000 genomes]
rs61429325	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6556823	0.86[ASN][1000 genomes]
rs6556824	0.93[ASN][1000 genomes]
rs6556829	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6556834	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6866771	0.93[ASN][1000 genomes]
rs6877616	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6879620	0.86[JPT][hapmap]
rs6879816	0.93[ASN][1000 genomes]
rs6880843	0.86[ASN][1000 genomes]
rs6881815	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6884138	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6889857	0.93[ASN][1000 genomes]
rs6890998	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6892853	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6895356	0.86[JPT][hapmap]
rs6898507	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs73133228	0.86[ASN][1000 genomes]
rs73133239	0.86[ASN][1000 genomes]
rs73133251	0.93[ASN][1000 genomes]
rs73133261	0.93[ASN][1000 genomes]
rs73133265	0.93[ASN][1000 genomes]
rs73133275	0.93[ASN][1000 genomes]
rs73133278	0.93[ASN][1000 genomes]
rs73133280	0.93[ASN][1000 genomes]
rs73133282	0.93[ASN][1000 genomes]
rs73133283	0.93[ASN][1000 genomes]
rs73133287	0.93[ASN][1000 genomes]
rs73133289	0.93[ASN][1000 genomes]
rs73133292	0.93[ASN][1000 genomes]
rs73133301	0.93[ASN][1000 genomes]
rs73135320	1.00[ASN][1000 genomes]
rs73135321	1.00[ASN][1000 genomes]
rs73135367	0.86[AMR][1000 genomes]
rs73135373	0.82[AMR][1000 genomes]
rs73135376	0.86[AMR][1000 genomes]
rs73772907	0.89[ASN][1000 genomes]
rs7702348	0.86[JPT][hapmap]
rs7702649	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs7712388	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7712899	0.93[ASN][1000 genomes]
rs7717718	0.86[JPT][hapmap]
rs7721168	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs7721509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs7727107	0.93[ASN][1000 genomes]
rs7736624	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9314086	0.87[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv1819334	chr5:92892591-92956733	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv4918	chr5:92898426-92943359	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1794960	chr5:92919821-92932305	Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1837322	chr5:92919821-92933747	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279473	GPR150	cis	cerebellum	SCAN
rs2279473	CETN3	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92922200-92934200	Weak transcription	HSMMtube	muscle
2	chr5:92924200-92935000	Weak transcription	Gastric	stomach
3	chr5:92926400-92932600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:92927000-92934600	Weak transcription	HUVEC	blood vessel
5	chr5:92929000-92932600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr5:92929200-92933000	ZNF genes & repeats	Spleen	Spleen
7	chr5:92929600-92932400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:92929600-92937800	Weak transcription	Right Atrium	heart
9	chr5:92930000-92932400	Weak transcription	Hela-S3	cervix
10	chr5:92930400-92932400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr5:92930600-92932400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:92930600-92934000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:92930600-92934600	Weak transcription	Fetal Kidney	kidney
14	chr5:92930800-92932600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:92930800-92933000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr5:92930800-92933000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:92930800-92933400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:92931000-92932800	Bivalent Enhancer	Fetal Stomach	stomach
19	chr5:92931000-92933000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr5:92931000-92933200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:92931000-92933200	Weak transcription	HepG2	liver
22	chr5:92931000-92933400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
23	chr5:92931000-92934200	Weak transcription	Pancreas	Pancrea
24	chr5:92931200-92932600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:92931200-92932800	Bivalent Enhancer	Fetal Lung	lung
26	chr5:92931200-92933000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:92931200-92933000	Strong transcription	NHLF	lung
28	chr5:92931200-92936000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:92931400-92932600	Bivalent Enhancer	Placenta	Placenta
30	chr5:92931400-92932800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
31	chr5:92931400-92933000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr5:92931600-92932400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
33	chr5:92931600-92932400	Bivalent Enhancer	Fetal Heart	heart
34	chr5:92931600-92932800	Bivalent Enhancer	Right Ventricle	heart
35	chr5:92931600-92935200	Weak transcription	Ovary	ovary
36	chr5:92931800-92932600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr5:92931800-92932600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:92931800-92933200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:92931800-92933800	Weak transcription	NH-A	brain
40	chr5:92932000-92932600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:92932000-92932600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
42	chr5:92932000-92932800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:92932000-92932800	Genic enhancers	Brain Germinal Matrix	brain
44	chr5:92932000-92933000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:92932000-92933000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr5:92932000-92933200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:92932200-92932400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr5:92932200-92932400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr5:92932200-92932400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
50	chr5:92932200-92932400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood

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